Multiple sequence alignment - TraesCS1D01G335300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G335300 chr1D 100.000 3301 0 0 1 3301 425298582 425301882 0.000000e+00 6096.0
1 TraesCS1D01G335300 chr1B 93.044 3321 139 39 1 3268 575440142 575443423 0.000000e+00 4769.0
2 TraesCS1D01G335300 chr1A 93.223 2169 92 20 1136 3268 520939490 520941639 0.000000e+00 3140.0
3 TraesCS1D01G335300 chr1A 86.817 1153 75 31 19 1144 520938363 520939465 0.000000e+00 1216.0
4 TraesCS1D01G335300 chr2A 95.679 486 19 2 1213 1698 746931081 746930598 0.000000e+00 780.0
5 TraesCS1D01G335300 chr2A 97.112 277 6 1 1720 1996 746927718 746927444 1.790000e-127 466.0
6 TraesCS1D01G335300 chr2A 88.701 354 23 10 2930 3268 746927418 746927067 1.830000e-112 416.0
7 TraesCS1D01G335300 chr3A 88.991 109 11 1 3160 3268 11635108 11635215 2.070000e-27 134.0
8 TraesCS1D01G335300 chr2D 98.039 51 1 0 1094 1144 532435019 532435069 4.540000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G335300 chr1D 425298582 425301882 3300 False 6096 6096 100.000000 1 3301 1 chr1D.!!$F1 3300
1 TraesCS1D01G335300 chr1B 575440142 575443423 3281 False 4769 4769 93.044000 1 3268 1 chr1B.!!$F1 3267
2 TraesCS1D01G335300 chr1A 520938363 520941639 3276 False 2178 3140 90.020000 19 3268 2 chr1A.!!$F1 3249
3 TraesCS1D01G335300 chr2A 746927067 746931081 4014 True 554 780 93.830667 1213 3268 3 chr2A.!!$R1 2055

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
545 570 0.318441 TCCTGTCGCTCTTCACTTGG 59.682 55.0 0.00 0.00 0.00 3.61 F
1009 1042 0.172352 TACGCACTGTGATCGATGCA 59.828 50.0 12.86 0.34 37.97 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 4926 0.464870 AGCAGCTAGAGACCATGCAG 59.535 55.0 0.00 0.00 39.34 4.41 R
2751 5693 0.523335 GCAACCGATCGAATTGGCAC 60.523 55.0 24.39 11.11 37.32 5.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 96 1.856012 GCAGATTATCAGTCGCCGC 59.144 57.895 0.00 0.00 0.00 6.53
103 123 3.535962 CGCCAGCTCCCTCTCTCC 61.536 72.222 0.00 0.00 0.00 3.71
105 125 2.837291 CCAGCTCCCTCTCTCCCG 60.837 72.222 0.00 0.00 0.00 5.14
106 126 3.535962 CAGCTCCCTCTCTCCCGC 61.536 72.222 0.00 0.00 0.00 6.13
107 127 4.067512 AGCTCCCTCTCTCCCGCA 62.068 66.667 0.00 0.00 0.00 5.69
108 128 3.535962 GCTCCCTCTCTCCCGCAG 61.536 72.222 0.00 0.00 0.00 5.18
109 129 3.535962 CTCCCTCTCTCCCGCAGC 61.536 72.222 0.00 0.00 0.00 5.25
110 130 4.067512 TCCCTCTCTCCCGCAGCT 62.068 66.667 0.00 0.00 0.00 4.24
124 144 1.215647 CAGCTAGCGGAACTTCGGT 59.784 57.895 9.49 0.00 43.51 4.69
182 202 2.481952 CGTTCTTCCTCAAAAGCTCAGG 59.518 50.000 0.00 0.00 0.00 3.86
238 261 2.930682 GCCCTATTAATTCGAGGCGATC 59.069 50.000 0.00 0.00 35.23 3.69
239 262 3.368531 GCCCTATTAATTCGAGGCGATCT 60.369 47.826 0.00 0.00 35.23 2.75
347 372 2.027385 GCCCAGATTCTGTGATTTCCC 58.973 52.381 12.54 0.00 0.00 3.97
348 373 2.292267 CCCAGATTCTGTGATTTCCCG 58.708 52.381 12.54 0.00 0.00 5.14
353 378 2.472695 TTCTGTGATTTCCCGGAGTG 57.527 50.000 0.73 0.00 0.00 3.51
394 419 7.652727 TGAGTCGTAGATCCTCAGATTAATTG 58.347 38.462 0.00 0.00 40.67 2.32
412 437 2.690778 GGCTAGGGTTGCACTTGCG 61.691 63.158 0.00 0.00 45.83 4.85
414 439 1.672356 CTAGGGTTGCACTTGCGCT 60.672 57.895 9.73 0.00 45.83 5.92
427 452 0.960364 TTGCGCTTGGAATCCTGGAC 60.960 55.000 9.73 0.00 0.00 4.02
448 473 3.524789 ACCCACATGGAAATCTCAGATGA 59.475 43.478 0.00 0.00 37.39 2.92
486 511 1.029681 GCTCCCGTGGTTTTCAACTT 58.970 50.000 0.00 0.00 0.00 2.66
526 551 3.374402 CGGTCTCGCCTCCTGTGT 61.374 66.667 0.00 0.00 34.25 3.72
527 552 2.574399 GGTCTCGCCTCCTGTGTC 59.426 66.667 0.00 0.00 0.00 3.67
528 553 2.574399 GTCTCGCCTCCTGTGTCC 59.426 66.667 0.00 0.00 0.00 4.02
529 554 1.979693 GTCTCGCCTCCTGTGTCCT 60.980 63.158 0.00 0.00 0.00 3.85
530 555 1.979155 TCTCGCCTCCTGTGTCCTG 60.979 63.158 0.00 0.00 0.00 3.86
531 556 2.203640 TCGCCTCCTGTGTCCTGT 60.204 61.111 0.00 0.00 0.00 4.00
532 557 2.219325 CTCGCCTCCTGTGTCCTGTC 62.219 65.000 0.00 0.00 0.00 3.51
533 558 2.262915 GCCTCCTGTGTCCTGTCG 59.737 66.667 0.00 0.00 0.00 4.35
545 570 0.318441 TCCTGTCGCTCTTCACTTGG 59.682 55.000 0.00 0.00 0.00 3.61
588 616 0.817013 TTTCTGCCCGGATTTGATGC 59.183 50.000 0.73 0.00 0.00 3.91
605 633 9.922305 GATTTGATGCTTACTAAATGAGTGTAC 57.078 33.333 0.00 0.00 39.39 2.90
783 812 0.671796 TCCGTGTACAGTGGACAGTG 59.328 55.000 8.93 4.46 37.75 3.66
805 834 3.179830 GTTGTAGACTGTAGTGCGATGG 58.820 50.000 0.00 0.00 0.00 3.51
1009 1042 0.172352 TACGCACTGTGATCGATGCA 59.828 50.000 12.86 0.34 37.97 3.96
1014 1047 2.412455 GCACTGTGATCGATGCATATGC 60.412 50.000 21.09 21.09 38.00 3.14
1543 1610 0.866061 GTCCATGATGGTCGTCGACG 60.866 60.000 31.30 31.30 39.03 5.12
1904 4829 1.252904 TTCCCCGTAGACAACCTCGG 61.253 60.000 0.00 0.00 42.22 4.63
2001 4926 1.518572 CACCTACGTCGTGGGCATC 60.519 63.158 25.93 0.00 37.72 3.91
2163 5091 4.042809 TGGGTGTGATGATCAAGTTAAGGT 59.957 41.667 0.00 0.00 0.00 3.50
2290 5221 5.483937 TGGGAGTCTCTGCTTAATAAGTTCA 59.516 40.000 1.68 0.00 0.00 3.18
2291 5222 6.156949 TGGGAGTCTCTGCTTAATAAGTTCAT 59.843 38.462 1.68 0.00 0.00 2.57
2377 5309 7.094508 TGTTTGCAACTCTTTCATGTTCTTA 57.905 32.000 0.00 0.00 0.00 2.10
2386 5318 6.591834 ACTCTTTCATGTTCTTACAATCCTCG 59.408 38.462 0.00 0.00 37.91 4.63
2391 5323 5.122239 TCATGTTCTTACAATCCTCGCTTTG 59.878 40.000 0.00 0.00 37.91 2.77
2392 5324 4.385825 TGTTCTTACAATCCTCGCTTTGT 58.614 39.130 0.00 0.00 39.32 2.83
2393 5325 4.451096 TGTTCTTACAATCCTCGCTTTGTC 59.549 41.667 0.00 0.00 37.29 3.18
2443 5376 7.039714 GGGGAGTTTCAATTTGTATGACTCTTT 60.040 37.037 16.05 0.00 0.00 2.52
2454 5387 5.924356 TGTATGACTCTTTTCACAAGGACA 58.076 37.500 0.00 0.00 0.00 4.02
2535 5470 5.952347 GGAAACCACCCTCTCATTCTTTAAT 59.048 40.000 0.00 0.00 0.00 1.40
2536 5471 6.437477 GGAAACCACCCTCTCATTCTTTAATT 59.563 38.462 0.00 0.00 0.00 1.40
2710 5651 7.094975 CGGGACTAGTGTGATTTGTCATTTAAA 60.095 37.037 0.00 0.00 0.00 1.52
2711 5652 8.739972 GGGACTAGTGTGATTTGTCATTTAAAT 58.260 33.333 0.00 0.00 0.00 1.40
2751 5693 3.435590 CCACAGTTGGGCACACAG 58.564 61.111 0.00 0.00 39.57 3.66
2772 5714 0.248215 GCCAATTCGATCGGTTGCAG 60.248 55.000 16.41 9.86 0.00 4.41
2983 5951 8.109705 AGATGTTACAAAGTGCACAATCAATA 57.890 30.769 21.04 4.99 0.00 1.90
3268 6254 6.656693 TGTTTTTAATTGGTGCCCCATATTTG 59.343 34.615 0.00 0.00 41.49 2.32
3269 6255 6.627087 TTTTAATTGGTGCCCCATATTTGA 57.373 33.333 0.00 0.00 41.49 2.69
3270 6256 6.627087 TTTAATTGGTGCCCCATATTTGAA 57.373 33.333 0.00 0.00 41.49 2.69
3271 6257 4.486125 AATTGGTGCCCCATATTTGAAC 57.514 40.909 0.00 0.00 41.49 3.18
3272 6258 2.612285 TGGTGCCCCATATTTGAACA 57.388 45.000 0.00 0.00 35.17 3.18
3273 6259 2.894731 TGGTGCCCCATATTTGAACAA 58.105 42.857 0.00 0.00 35.17 2.83
3274 6260 3.448934 TGGTGCCCCATATTTGAACAAT 58.551 40.909 0.00 0.00 35.17 2.71
3275 6261 3.197333 TGGTGCCCCATATTTGAACAATG 59.803 43.478 0.00 0.00 35.17 2.82
3276 6262 3.432046 GGTGCCCCATATTTGAACAATGG 60.432 47.826 0.00 0.00 39.95 3.16
3277 6263 3.197549 GTGCCCCATATTTGAACAATGGT 59.802 43.478 4.75 0.00 38.83 3.55
3278 6264 3.843027 TGCCCCATATTTGAACAATGGTT 59.157 39.130 4.75 0.00 38.83 3.67
3279 6265 4.288105 TGCCCCATATTTGAACAATGGTTT 59.712 37.500 4.75 0.00 38.83 3.27
3280 6266 4.635324 GCCCCATATTTGAACAATGGTTTG 59.365 41.667 4.75 0.00 38.83 2.93
3281 6267 4.635324 CCCCATATTTGAACAATGGTTTGC 59.365 41.667 4.75 0.00 38.83 3.68
3282 6268 5.243981 CCCATATTTGAACAATGGTTTGCA 58.756 37.500 4.75 0.00 38.83 4.08
3283 6269 5.704515 CCCATATTTGAACAATGGTTTGCAA 59.295 36.000 0.00 0.00 38.83 4.08
3284 6270 6.348376 CCCATATTTGAACAATGGTTTGCAAC 60.348 38.462 0.00 0.00 38.83 4.17
3285 6271 6.427547 CCATATTTGAACAATGGTTTGCAACT 59.572 34.615 0.00 0.00 37.36 3.16
3286 6272 5.738118 ATTTGAACAATGGTTTGCAACTG 57.262 34.783 0.00 0.00 37.36 3.16
3287 6273 4.462508 TTGAACAATGGTTTGCAACTGA 57.537 36.364 0.00 0.00 37.36 3.41
3288 6274 4.669206 TGAACAATGGTTTGCAACTGAT 57.331 36.364 0.00 0.00 37.36 2.90
3289 6275 4.619973 TGAACAATGGTTTGCAACTGATC 58.380 39.130 0.00 0.00 37.36 2.92
3290 6276 4.099113 TGAACAATGGTTTGCAACTGATCA 59.901 37.500 0.00 0.00 37.36 2.92
3291 6277 4.669206 ACAATGGTTTGCAACTGATCAA 57.331 36.364 0.00 0.00 36.22 2.57
3292 6278 5.217978 ACAATGGTTTGCAACTGATCAAT 57.782 34.783 0.00 0.00 36.22 2.57
3293 6279 6.343716 ACAATGGTTTGCAACTGATCAATA 57.656 33.333 0.00 0.00 36.22 1.90
3294 6280 6.757237 ACAATGGTTTGCAACTGATCAATAA 58.243 32.000 0.00 0.00 36.22 1.40
3295 6281 7.215789 ACAATGGTTTGCAACTGATCAATAAA 58.784 30.769 0.00 0.00 36.22 1.40
3296 6282 7.714377 ACAATGGTTTGCAACTGATCAATAAAA 59.286 29.630 0.00 0.00 36.22 1.52
3297 6283 7.656707 ATGGTTTGCAACTGATCAATAAAAC 57.343 32.000 0.00 4.10 0.00 2.43
3298 6284 6.577103 TGGTTTGCAACTGATCAATAAAACA 58.423 32.000 0.00 10.30 0.00 2.83
3299 6285 7.044181 TGGTTTGCAACTGATCAATAAAACAA 58.956 30.769 0.00 6.51 0.00 2.83
3300 6286 7.224362 TGGTTTGCAACTGATCAATAAAACAAG 59.776 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.204292 TCCTGTTGATGATAGCTGACTAGT 58.796 41.667 0.00 0.00 0.00 2.57
105 125 2.167861 CCGAAGTTCCGCTAGCTGC 61.168 63.158 13.93 0.00 38.57 5.25
106 126 1.078759 CACCGAAGTTCCGCTAGCTG 61.079 60.000 13.93 6.46 0.00 4.24
107 127 1.215647 CACCGAAGTTCCGCTAGCT 59.784 57.895 13.93 0.00 0.00 3.32
108 128 1.080025 ACACCGAAGTTCCGCTAGC 60.080 57.895 4.06 4.06 0.00 3.42
109 129 1.352156 GCACACCGAAGTTCCGCTAG 61.352 60.000 0.00 0.00 0.00 3.42
110 130 1.373748 GCACACCGAAGTTCCGCTA 60.374 57.895 0.00 0.00 0.00 4.26
124 144 2.741985 CGATTGCCTCCGTGCACA 60.742 61.111 18.64 0.00 41.88 4.57
182 202 1.673665 CTGAAGTGACCCTGGCTGC 60.674 63.158 0.00 0.00 0.00 5.25
215 238 0.796927 GCCTCGAATTAATAGGGCGC 59.203 55.000 0.00 0.00 0.00 6.53
238 261 1.227497 GCTTCTCCCCGCAGATCAG 60.227 63.158 0.00 0.00 0.00 2.90
239 262 1.687146 AGCTTCTCCCCGCAGATCA 60.687 57.895 0.00 0.00 0.00 2.92
347 372 4.170723 GGAGCTCGAAACACTCCG 57.829 61.111 7.83 0.00 40.59 4.63
353 378 2.990514 GACTCAAGAAGGAGCTCGAAAC 59.009 50.000 7.83 0.00 38.50 2.78
394 419 2.690778 CGCAAGTGCAACCCTAGCC 61.691 63.158 3.87 0.00 42.21 3.93
412 437 0.681243 GTGGGTCCAGGATTCCAAGC 60.681 60.000 14.17 0.00 0.00 4.01
414 439 1.005805 CATGTGGGTCCAGGATTCCAA 59.994 52.381 14.17 7.31 0.00 3.53
427 452 4.160642 TCATCTGAGATTTCCATGTGGG 57.839 45.455 0.00 0.00 35.41 4.61
448 473 5.055812 GGAGCTTCAAAATCAGATCGAGAT 58.944 41.667 0.00 0.00 0.00 2.75
525 550 1.423395 CAAGTGAAGAGCGACAGGAC 58.577 55.000 0.00 0.00 0.00 3.85
526 551 0.318441 CCAAGTGAAGAGCGACAGGA 59.682 55.000 0.00 0.00 0.00 3.86
527 552 0.034059 ACCAAGTGAAGAGCGACAGG 59.966 55.000 0.00 0.00 0.00 4.00
528 553 2.724977 TACCAAGTGAAGAGCGACAG 57.275 50.000 0.00 0.00 0.00 3.51
529 554 3.678056 AATACCAAGTGAAGAGCGACA 57.322 42.857 0.00 0.00 0.00 4.35
530 555 3.371285 GGAAATACCAAGTGAAGAGCGAC 59.629 47.826 0.00 0.00 38.79 5.19
531 556 3.596214 GGAAATACCAAGTGAAGAGCGA 58.404 45.455 0.00 0.00 38.79 4.93
532 557 2.348666 CGGAAATACCAAGTGAAGAGCG 59.651 50.000 0.00 0.00 38.90 5.03
533 558 2.678336 CCGGAAATACCAAGTGAAGAGC 59.322 50.000 0.00 0.00 38.90 4.09
574 602 1.680338 AGTAAGCATCAAATCCGGGC 58.320 50.000 0.00 0.00 0.00 6.13
588 616 4.733887 CCTCGCGTACACTCATTTAGTAAG 59.266 45.833 5.77 0.00 35.76 2.34
683 711 4.815269 ACTGAGTTTAGTGAGCTTGCTAG 58.185 43.478 0.00 0.00 0.00 3.42
684 712 4.280929 TGACTGAGTTTAGTGAGCTTGCTA 59.719 41.667 0.00 0.00 0.00 3.49
685 713 3.070159 TGACTGAGTTTAGTGAGCTTGCT 59.930 43.478 0.00 0.00 0.00 3.91
783 812 3.179830 CATCGCACTACAGTCTACAACC 58.820 50.000 0.00 0.00 0.00 3.77
798 827 1.960763 GCGGCATGTATCCATCGCA 60.961 57.895 0.00 0.00 41.42 5.10
799 828 0.389817 TAGCGGCATGTATCCATCGC 60.390 55.000 1.45 0.00 41.84 4.58
805 834 2.049228 GTACGTGTAGCGGCATGTATC 58.951 52.381 15.20 8.34 46.52 2.24
1009 1042 3.053917 TGATGATATGGCCTGCTGCATAT 60.054 43.478 3.32 0.00 43.89 1.78
1014 1047 3.693085 GGTAATGATGATATGGCCTGCTG 59.307 47.826 3.32 0.00 0.00 4.41
1020 1053 7.337689 TCAAGCATAAGGTAATGATGATATGGC 59.662 37.037 0.00 0.00 0.00 4.40
1215 1282 1.968540 GGTCCTCACCTTGCTGTGC 60.969 63.158 0.00 0.00 40.00 4.57
1323 1390 2.915659 TCGACGACCTTGCTGGGT 60.916 61.111 0.00 0.96 43.07 4.51
1365 1432 4.919653 GGCAGCTTGTCGATCTCA 57.080 55.556 0.00 0.00 0.00 3.27
2001 4926 0.464870 AGCAGCTAGAGACCATGCAG 59.535 55.000 0.00 0.00 39.34 4.41
2163 5091 1.895966 TGCACAGTGGCTGCAAAAA 59.104 47.368 5.98 0.00 41.70 1.94
2218 5149 4.083324 ACAAAGCCAGTCAATACATGAACG 60.083 41.667 0.00 0.00 40.50 3.95
2291 5222 8.621286 GGAGATACAAAACTCACAAGAGAAAAA 58.379 33.333 0.00 0.00 44.98 1.94
2377 5309 1.531149 CAACGACAAAGCGAGGATTGT 59.469 47.619 0.00 0.00 42.18 2.71
2386 5318 3.075884 TGTATAACCCCAACGACAAAGC 58.924 45.455 0.00 0.00 0.00 3.51
2391 5323 7.739498 ATTAATCATGTATAACCCCAACGAC 57.261 36.000 0.00 0.00 0.00 4.34
2392 5324 7.229707 CCAATTAATCATGTATAACCCCAACGA 59.770 37.037 0.00 0.00 0.00 3.85
2393 5325 7.367285 CCAATTAATCATGTATAACCCCAACG 58.633 38.462 0.00 0.00 0.00 4.10
2443 5376 7.969536 TTGAAATTGTTTTTGTCCTTGTGAA 57.030 28.000 0.00 0.00 0.00 3.18
2497 5432 1.002773 GGTTTCCCGAAAGAGTAGGCA 59.997 52.381 0.00 0.00 0.00 4.75
2535 5470 6.918067 ACTCGGATATGACCATTCTGATAA 57.082 37.500 0.00 0.00 0.00 1.75
2536 5471 6.918067 AACTCGGATATGACCATTCTGATA 57.082 37.500 0.00 0.00 0.00 2.15
2710 5651 6.127253 GGGTCACAAAATCTTGAATGATCCAT 60.127 38.462 0.00 0.00 38.13 3.41
2711 5652 5.185635 GGGTCACAAAATCTTGAATGATCCA 59.814 40.000 0.00 0.00 38.13 3.41
2751 5693 0.523335 GCAACCGATCGAATTGGCAC 60.523 55.000 24.39 11.11 37.32 5.01
2818 5760 9.945904 GCTTAACTGCTTATAGGAATTATAGGT 57.054 33.333 0.00 0.00 0.00 3.08
2909 5851 5.128663 AGGCAAAATGTTCAGTAAAACTGGT 59.871 36.000 7.18 0.00 45.94 4.00
3133 6118 7.974243 AAATGATGTTTTTCTTTTGCAAAGC 57.026 28.000 12.41 0.00 0.00 3.51
3171 6157 6.423776 AAAATCAAGCCATTTTCCTTCTCA 57.576 33.333 0.00 0.00 31.53 3.27


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.